David Cameron's new coalition government was embarrassed yesterday by the special immigration court ruling in the case of Abid Naseer and Ahmed Faraz Khan. It seems that the two Pakistani students are simultaneously a threat to the security of Britain, and cannot be sent home for fear that their own police might threaten their security with a spot of torture.

Tricky, isn't it? Welcome to government, government. What will happen next? The Guardian's experts in this field, Ian Cobain and Richard Norton-Taylor, are prompted to highlight the dilemma faced by Nick Clegg and his fellow Lib Dem minister Chris Huhne.

If Naseer and Khan, both 23, cannot be deported but cannot be charged with terrorist offences either – the hard evidence isn't there, so we are told – they may have to be subject to control orders.

Why? Because – as we are also told – they are serious al-Qaida operatives who had cast a murderous eye on Manchester's Arndale shopping centre, itself the rebuilt fruit of another terrorist bomb, the IRA's.

But Nick Clegg and Huhne have denounced the control order option as a Kafkaesque nightmare: expensive, illiberal and ineffectual. How those spine-tingling words must have rolled off their lips in the good old days of opposition ... Delicious.

Alas, be careful what you wish for. The pair are now in government – Clegg and Huhne, not Naseer and Khan – facing harder choices. They are in partnership with a Tory party, part of whose detox exercise was to assert a more wholesome view of civil liberties than the one they – often wrongly – attributed to Labour.

As Patrick Wintour and Andrew Sparrow report, Clegg is making a speech on another aspect of the civil rights agenda – the coalition's own ticking car bomb – this morning: the fantasy Tory plan to replace the European convention on human rights (ECHR) with a domestic bill of rights. Tick, tick, tick.

Free speech, fair and open trials, an end to any complicity in torture ... There should be a return to core human rights values that have been central to British life, she says. All good stuff, but the civil liberties lobby is not blameless either.

For one thing (we will leave the Unite union and BA aside for a moment), it has never taken its opponents' core case seriously enough. Namely that there are nasty people out there – usually immature young men with not much of a love life – who want to do serious harm to innocent citizens in the name of some pretty wacky ideas.

These create what we call dilemmas, minister. In office it is hard to be both effective and loved for long by such vested interests as the civil liberties lobby. It tends to be distinctly middle-to-upper-middle class in its concerns, which are more about torture in foreign lands than money-raising CCTV cameras or bricks thrown through council house windows late at night.

May passed a useful test this morning, very much a civil liberties test in the national interest, when she stood up to John Humphrys browbeating her on behalf of mythical middle Britain – aka the Daily Mail – on Radio 4's Today programme. Have you Tories abandoned the repeal of the HRA, he kept asking. We are in talks, she kept answering. Well done, Tess.

But there is a long way to go and so many directions to travel in at this vital early stage of the coalition, where new ministers and their officials are testing each other's strengths.

The Cleggs, Mays, Huhnes and Dominic Grieves (the new attorney general strikes me as sound and thoughtful) will bring in new thinking and influences. Who knows, they may be able to cut the Gordian Knot – that's nothing to do with Gordon Brown, dears – that has defeated Whitehall for years: reconciling liberty with security in honourable ways.

But don't hold your breath too long. These problems existed long before New Labour, when Michael Howard set the tone as home secretary for an aggressive bidding war on law and order that Blair embraced. The stats say most crime has fallen sharply, but it does us little good if we do not feel safer.

As for the Naseer-Khan case, it is more Alice in Wonderland than most, as much cock-up as conspiracy. Of the 10 Pakistanis rapidly arrested after then-top-copper Bob Quick left a secret memo visible to cameras outside No 10, eight chose to go home after protesting their total innocence. As far as we know, they appear to be unmolested.

What should we conclude from that? Or from the fact that yesterday's court did not believe the protestations of equally innocent conduct – supported by that saintly lawyer Gareth Peirce – in discussing marriage, not high explosive options, during email chats with al.qaida.net?

I don't know either. The circumstantial evidence has not been tested in open court, which is unsatisfactory. But do not dismiss it out of hand. Clegg and Huhne may now be reading files that make them slump, head in hands, like Gordon Brown on the Jeremy Vine show.